---
type: Conversation
title: Private channel session 1522
description: "slack conversation, 14 messages, 2021-06-19."
tags:
  - conversation
  - slack
medium: slack
message_count: 14
started_at: "2021-06-19T10:10:18"
ended_at: "2021-06-19T12:03:01"
duration_seconds: 6763
sources:
  - { id: slack_pm, resource: /sources/slack-pm.md, title: Slack / Private Message Drop, author: "process:senate-hsgac-release" }
generated: { by: randpaul-corpus-pipeline/1.0, at: "2026-08-01T12:42:27Z" }
status: stable
---

A slack conversation of 14 messages spanning 1h 52m.

# Metadata

- **Started:** 2021-06-19T10:10:18
- **Ended:** 2021-06-19T12:03:01
- **Duration:** 1h 52m
- **Participants:** 2
- **Source:** [slack_pm](/sources/slack-pm.md)
- **Pages:** 945-946

# Participants

* [Andrew Rambaut](/people/andrew-rambaut.md)
* [Edward C. Holmes](/people/edward-c-holmes.md)
* [Kristian G. Andersen](/people/kristian-g-andersen.md)
* [Robert F. Garry](/people/robert-f-garry.md)

# Transcript

**[2021-06-19T10:10:18] Robert F. Garry:** Bloom - please read !channel IMPORTANT [shared file(s): paper.pdf]

**[2021-06-19T10:15:31] Robert F. Garry:** "However, the current study suggests that at least in one case, the trusting structures of science have been abusedto obscure sequences relevant to the early spread of SARS-CoV-2 in Wuhan. A careful re-evaluation of otherarchived forms of scientific communication, reporting, and data could shed additional light on the early emergence ofthe virus."

**[2021-06-19T10:33:49] Andrew Rambaut:** Is it deep sequencing data? Or amplicons?

**[2021-06-19T10:35:40] Andrew Rambaut:** Amplicons - ```The study describes an approach to diagnose infection withSARS-CoV-2 and other respiratory viruses by nanopore sequenc-ing. This approach involved reverse-transcription of total RNAfrom swab samples, followed by PCR with specific primers togenerate amplicons covering portions of the viral genome. Theseamplicons were then sequenced on an Oxford Nanopore Grid-ION, and infection was diagnosed if the sequencing yieldedsufficient reads aligning to the viral genome. Importantly, thestudy notes that this approach yields information about thesequence ofthe virus as well enabling diagnosis of infection```At least 2 of the mutations talked about are in or immediately adjacent to ARTIC…

**[2021-06-19T10:35:55] Robert F. Garry:** Wang _et al._ (2020a) sequenced PCR amplicons covering nu- cleotide sites 21,563 to 29,674 of the SARS-CoV-2 genome, which spans from the start of the spike gene to the end of ORF10. They also sequenced a short amplicon generated by nested PCR that covered a fragment of ORF1ab spanning sites 
15,080 to 15,550. In this paper, I only analyze the region from spike through ORF10 because this is a much longer contiguous sequence and theamplicons were generated by conventional rather than nested PCR. I slightly trimmed the region of interest to21,570 to 29,550 because many samples had poor coverage at the termini."

**[2021-06-19T10:36:40] Andrew Rambaut:** Ah - OK so not the ARTIC amplicons then

**[2021-06-19T10:39:07] Robert F. Garry:** WA1 is lineage A and has bat-like T8782 and C28144 plus another bat-like snp - what mutation is this?

**[2021-06-19T10:41:05] Robert F. Garry:** More top secret stuff - Tony and Francis have arranged a call with Jesse tomorrow - need to sort this out...

**[2021-06-19T10:42:47] Robert F. Garry:** C18060T?

**[2021-06-19T11:33:37] Andrew Rambaut:** ```But the earliest known SARS-CoV-2 sequences, whichare mostly derived from the Huanan Seafood Market, are no-tably more different from these bat coronaviruses than othersequences collected at later dates outside Wuhan.``` This is incorrect - WA1 is from Wuhan

**[2021-06-19T11:34:38] Robert F. Garry:** *Yes from your earlier post (Numbering off by 1) Andrew Rambaut* [12:11 PM] Wuhan-Hu-1: T:8781:C|T:18059:C|C:28143:T WH04: T:18059:C WA1: 0:

**[2021-06-19T11:34:43] Andrew Rambaut:** So it is they are notably (2 or 3 mutations) more distant from RATG13 than other viruses in Wuhan at the same time

**[2021-06-19T11:56:30] Robert F. Garry:** Yes - he's got WA1 in the mix, but yes definitely WA1 early Wuhan for sure. I'm thinking Jesse making much ado about nothing - it's lineage A going to lineage B with WA1 from Wuhan ancestral.

**[2021-06-19T12:03:01] Robert F. Garry:** "Rambaut _et al._ (2020) suggest that viruses from the clade labeled "B" in Figure 4 may just "happen" to have been sequenced first, but that other SARS-CoV-2 sequences are really more ancestral as implied by phylogenetic rooting." Uhhh Rambaut is right about this...